Hello I was analysing some data using StingTie, initially was working fine, then at some point I start getting an error (it is reported as a tool error). I indeed tried to run again StringTie for a samples that had worked fine and now I get a tool error.
Can anyone help me fixing this?
Best,
P
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I actually figure out that there is the error only when running StringTie with the output for differential expression analysis using DESeq2.
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It is not clear what tool is presenting with an error. DE analysis is covered in much detail in the Galaxy Tutorials and might be able to help you to solve the problem.
Troubleshooting overview:
Troubleshooting FAQ, including how to check for input problems:
The subsection of that first post that covers using tutorials to troubleshoot usage problems. You’ll find DE analysis under the “Transcriptomics” tutorial group.
Hope that helps!
Hi,
I have used HISAT (for alignment)-Stringtie(Assembly). After analyzing with stringtie there are five output.They are
Intron to transcript mapping
Exon to transcript mapping
Transcript level expression measurement
Coverage and
Assembled transcripts.
I merged the assembled GTF files using both Stringtie and cuffmerge. I tried both merged files (Stringtie and cuffmerge) in cuffdiffs both gave me errors. I tried individual GTF assembled files from stringtie and used in DES2 and EdgeR. All of them gave me errors. Can someone guide me if i doing something wrong? If the process i am following is correct can you please suggest me the possible alternatives for differential expression using string tie.
Thanks in advance
Update: This question has come up a few times recently, so this is a fresh example of how to use HISAT2 → Stringtie → DESeq2
Technically…
- all of the data should be in collections with group tags, but the way this example is organized makes the usage a bit clearer to review in the context of someone else’s history just based on higher level tags. GTN search = tags
- for real data, be sure to do some QA on the reads before mapping! GTN search = quality
- also double check strand! this is covered in the Transcriptomics tutorials a few places
This only captures known features. For novel features, consider following the methods in the GTN tutorial here instead: De novo transcriptome reconstruction with RNA-Seq
Anyone can copy/import to review closer. Please pay attention to the data formats (especially the GTF) and the parameters used with all tools.
Shared history: https://usegalaxy.org/u/jen-galaxyproject/h/stringtie-2-deseq2-gene-de